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According to Memory Alpha, Chakotay graduated from Starfleet Academy in 2348, meaning he was in Starfleet for a good twenty years before leaving to join the Maquis.

Doesn't that make him more experienced than Janeway? And why didn't Janeway just restore his rank when he joined Voyager, instead of giving him that dumb provisional rank insignia, for all seven years?

According to Memory Alpha, Chakotay graduated from Starfleet Academy in 2348, meaning he was in Starfleet for a good twenty years before leaving to join the Maquis.

Doesn't that make him more experienced than Janeway? And why didn't Janeway just restore his rank when he joined Voyager, instead of giving him that dumb provisional rank insignia, for all seven years?

How do you know she didn't offer them to him? All we know is that he wore provisional pips and that there was an agreement between them to run Voyager as a Starfleet ship. Anything else is conjecture. I can actually think of reasons why he would offer to be provisional Starfleet, and why he would have encouraged the Maquis to be Starfleet also. You are also making the assumption that years in Starfleet are equal, I assure you that even in the real world, years of general experience are always beat out by specific experience. Meaning, apparently (again speculation because of lack of specific knowledge) Chakotay had not commanded a Starfleet ship, the back story originally projected for Janeway; was that she had commanded a ship previously. There is also no evidence that Chakotay never held Starfleet rank above Commander while Janeway was actually a Captain.

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"My name is Matai Shang and I do not exist, indeed I work very hard at it."

Voyager was Janeway's ship. She was the captain. It doesn't matter how long Chakotay served or what his rank was before he resigned, at the time she offered him the 2nd chair he was not a Starfleet officer. The compromise was for the Starfleet and Maquis crew to serve together as one to find a way home. But it was still Janeway's ship.

If you quit your job to spend a year climbing a mountain or whatever, you have given up your claim to that job and any benefits that went with it. If you come back and the company offers to rehire you but at a lower pay grade, it's up to you to decide whether or not you take the job.

Wasn't Weasely's pip (initially) off one of the other command officers neck?

Wes' rank was completely made up.

You'd have to wonder what would happen when he tried to boss around the enlisted twice his age?

Captain Chakotay Wore Pips in Before and After.

From a costume point of view, they couldn't be bothered making a Captains Maquis provisional rank badge, from a Captain Chakotay's point of view "screw that bipolar ghost #####'s ass."

canon conflicts.

From shattered

JANEWAY: Why do I get the feeling that's an understatement? It doesn't seem like
my first command is shaping up the way I expected.

From Revulsion

JANEWAY: The first time I met Tuvok he dressed me down in front of three Starfleet admirals for failing to observe proper tactical procedures during my first command. My human ego took a little bruising, but of course he was right. Over the past nine years I've come to rely on his insightful and unfailingly logical advice. For outstanding services, Chief Tactical and Security Officer, it's my pleasure to grant you the rank of Lieutenant Commander. Congratulations, Tuvok.

Neelix would have been a better captain than janeway, the computer would have made a better captain, one of Harry Kims stools would have made a better captain...but you still can't realistically expect a member of the Maquis, who abandoned star fleet to take over a ship just because he is more experienced

Starfleet probably bought him by promising him the two pips. Janeway thus felt she had the authority to deliver them after the capture-Chakotay-and-relieve-Tuvok mission went (mostly) as planned; that'd be different from Janeway giving pips to the Maquis on her own account.

You'd have to wonder what would happen when [Wesley] tried to boss around the enlisted twice his age?

The officers he bossed around in "Pen Pals" weren't all that much younger. And if O'Brien is any indication, enlisted in the future still cower before the bright shine of collar brass.

As for Janeway's "first command", it could be a tale of two meanings: first time commanding a mission vs. first time commanding a ship. There's something of a distinction there; even the Spock/McCoy agreement that the command of the Galileo was Spock's first could fall in this category, the shuttle indeed being the first spacecraft whose crew Spock commanded even though the Vulcan had commanded a large number of missions before.